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You don't have to remove the old version of ROS to start using a new one. Multiple versions can happily be installed next to each other. E.g. the cturtle version is installed in /opt/ros/cturtle, and the diamondback version is installed in /opt/ros/diamondback. You can switch between versions by setting your environment:

source /opt/ros/diamondback/setup.bash

If you do want to remove a version of ROS, you should use the apt tools instead of manually removing files:

sudo apt-get remove ros-cturtle-ros